tbuckley/cabot-search huggingface dataset:
NIMG-24. RECURRENT OLIGODENDROGLIOMA DEMONSTRATES EARLY INCREASE IN CEREBRAL BLOOD FLOW AND NORMALIZATION IN RESPONSE TO TREATMENT
Authors: Alp Oztek, Jalal Andre, Tresa McGranahan
Journal: Neuro-Oncology (2023)

Abstract Oligodendrogliomas, molecularly defined by the presence of both IDH mutation and 1p/19q codeletion, are more treatment responsive than other gliomas, and due to short capillary segments, demonstrate elevated CBF regardless of grade or contrast enhancement. Arterial Spin Labeling (ASL) allows noninvasive perfusion imaging assessment of cerebral blood flow (CBF) without contrast administration. Changes in CBF are recognized in association with malignant transformation of gliomas however in the setting of treatment, CBF has only been studied to assist in differentiating radiation treatment effect from progressive glioma. This single center retrospective study was undertaken to evaluate if CBF, measured by ASL, might normalize following treatment of recurrent oligodendrogliomas. Clinical database query identified 151 patients with molecularly confirmed oligodendroglioma, 34 of which had available ASL imaging. Expert reader review of all available MRI sequences, blinded to treatment timeline, were performed by two independent radiologists at a PACS station. There were 6 radiographic recurrences identified and in 5/6 CBF was the first radiographic change. Contrast enhancement did not develop for 1.5-12 months after change in CBF for 4/5 recurrences. ASL imaging before and after non-surgical therapy for recurrent disease was available for 4 patients. Two patients were treated with lomustine, one with bevacizumab and one with proton re-radiation. By the second MRI following treatment initiation, all patients had normalization of CBF. At the first post treatment MRI, 3/4 of patients demonstrated normalization of CBF while only 2/4 demonstrated normalization of dynamic susceptibility contrast-derived cerebral blood volume. During the subsequent 6 months, FLAIR hyperintensities remained stable in all patients. This work supports further study if normalization of ASL-derived CBF may be an early radiographic biomarker for response to treatment, especially in non or minimally enhancing recurrent gliomas.
NIMG-45. EXTERNAL EVALUATION OF A MACHINE LEARNING MODEL EMPLOYING RADIOMICS TO IDENTIFY REGIONS OF LOCAL RECURRENCE IN GLIOBLASTOMA FROM POSTOPERATIVE MRI
Authors: Santiago Cepeda, Luigi Luppino, Marek Wodsinski, Ole Solheim, Angel Perez-Nuñez, Sergio Garcia-Garcia, Anna Karlberg, Live Eikenes, Tomas Zamora, Rosario Sarabia, Ignacio Arrese, Samuel Kuttner
Journal: Neuro-Oncology (2023)

Abstract The standard surgical goal for operable glioblastomas worldwide is the complete excision of the enhancing tumor. Nevertheless, the peritumoral region harbors infiltrating cells leading to recurrence. Our study aims to evaluate a predictive model designed to predict potential regions of recurrence using voxel-based radiomics analysis on postoperative magnetic resonance imaging (MRI). This retrospective, multi-institutional study involved glioblastoma patients who had undergone complete resection. The training cohort comprised 49 patients from two Spanish institutions, with model evaluation using an external dataset of 27 patients from a Norwegian institution and the public Ivy-Gap dataset. We used follow-up MRI scans for ground truth definition of recurrence, while postoperative multiparametric MRI scans provided the data for extracting voxel-based radiomic features. Our method employed an unsupervised, hybrid approach, which combined a deep neural network and instance optimization, to align the MRI sequences for each patient, registering the follow-up with the postoperative scans. To generate ground truth labels, we segmented the peritumoral region in the postoperative scans, identified as the area showing T2/FLAIR signal alterations, in addition to the enhancing tumor visible in the registered follow-up scan. Overlapping voxels between the peritumoral and enhancing tumor regions were classified as recurrence, while non-overlapping voxels were labeled as nonrecurrence. Radiomic features were subsequently extracted from the postoperative peritumoral region. We trained four machine learning classifiers to predict recurrence. Among these, the Categorical Boosting (CatBoost) classifier demonstrated excellent performance on the test dataset, achieving an average area under the curve (AUC) of 0.83 ± 0.07, and an accuracy of 0.80 ± 0.12, based on voxel-wise comparison with the ground truth. Our study resulted in a method that accurately predicts the area of future tumor recurrence in glioblastoma patients' MRI scans. This innovation could potentially tailor surgical and radiotherapy treatment strategies to these specific areas, possibly extending patient survival.
BIOM-60. CONCATEMERIC CONSENSUS ERROR CORRECTED SEQUENCING (CCEC-SEQ) APPROACH FOR PLASMA CELL-FREE TUMOR DNA-BASED TREATMENT RESPONSE MONITORING IN PATIENTS WITH BRAIN TUMORS
Authors: Jack Wadden, Vishal John, Rayan Aittaleb, Carl Koschmann
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Diffuse midline gliomas (DMG) are aggressive and universally fatal with a median survival rate of only 9-12 months. MRIs can be difficult to interpret due to diffuse disease and radiation-induced swelling. Recent work has shown that liquid biopsy of cell-free tumor DNA (cf-tDNA) in patient plasma using digital droplet PCR (ddPCR) might help supplement radiographic monitoring, and enable more quantitative, low-cost, rapid tests. Nanopore sequencing has been employed to quickly and affordably measure and track treatment response in DMG patient cerebrospinal fluid (CSF) where cf-tDNA variant allele fractions are high ( &amp;gt;1%). However, plasma cf-tDNA signal is much lower than CSF (typically &amp;lt; 0.5%), and no platforms have demonstrated the feasibility of quickly (&amp;lt; 1day) sequencing brain tumor cf-tDNA in plasma samples to our knowledge. METHODS To solve these problems, we have developed a same-day, multiplexed, concatemeric consensus error corrected (CCEC-Seq) assay approach for Nanopore sequencing. We combine multiplex PCR and loop-mediated isothermal amplification (LAMP) to capture short cf-tDNA fragments and concatemerize them. Sequenced concatemer segments should agree, and allow informatic consensus error correction, reducing Nanopore error rates. RESULTS We generated a multiplex (n = 8) DMG hotspot loci panel, which was able to reduce sequencing false positive call rates by 3.1x-10.8x. We were able to employ the CCEC-Seq technique on serial plasma samples from a patient with DMG with H3.3K27M mutation undergoing treatment with ONC201 with results comparable to a previously validated ddPCR assay. Ongoing work will apply this multiplex CCEC-Seq panel to a larger cohort of serial DMG plasma samples. CONCLUSION To our knowledge, this is the first demonstration of same-day, sequencing-based, liquid biopsy protocol for a plasma sample from a brain tumor patient. This approach has the potential to greatly reduce resource requirements, and ease of operation for liquid biopsy for DMG and other brain tumor disease monitoring.
PATH-19. PROGNOSTIC FACTORS, RESPONSE TO TREATMENT, AND OUTCOME OF PATIENTS WITH ISOCITRATE DEHYDROGENASE (IDH)-MUTANT ASTROCYTOMA, CNS WHO GRADE 4
Authors: Michael Weller, Jörg Felsberg, Bettina Hentschel, Dorothee Gramatzki, Nadezhda Kubon, Marietta Wolter, Patrick Roth, Dietmar Krex, Ulrich Herrlinger, Manfred Westphal, Joerg-Christian Tonn, Luca Regli, Claude-Alain Maurage, Andreas von Deimling, Torsten Pietsch, Emilie Le Rhun, Guido Reifenberger
Journal: Neuro-Oncology (2023)

Abstract PURPOSE To study disease characteristics, prognostic markers and outcome in patients with isocitrate dehydrogenase (IDH)-mutant astrocytoma by CNS WHO grade. EXPERIMENTAL DESIGN We determined molecular biomarkers and assembled clinical and outcome data in a cohort of 258 patients with IDH-mutant astrocytomas (114 CNS WHO grade 2, 73 CNS WHO grade 3, 71 CNS WHO grade 4) confirmed by central pathology review. RESULTS The median age for astrocytoma, IDH mutant, CNS WHO grade 4, was 37 (range: 23-79 years) and similar to patients with CNS WHO grade 2 or 3 tumors. Karnofsky performance status at diagnosis inversely correlated with CNS WHO grade (p&amp;lt; 0.001). Despite more intensive treatment upfront with higher grade, CNS WHO grade was strongly prognostic: median overall survival was 22.2 years (95% n.a.) for grade 2, 8.1 years (95% 5.4-10.8) for grade 3 and 4.7 years (95% 3.4-6.0) for grade 4. Among patients with CNS WHO grade 4 astrocytoma, median overall survival was 5.5 years (95% 4.3-6.7) without (n=58) versus 1.8 years (95% 0-4.1) with (n=12) homozygous CDKN2A homozygous deletion. Reduced global DNA methylation as indicated by LINE-1 methylation levels was strongly associated with CNS WHO grade 4 (p&amp;lt; 0.001) and poor outcome among IDH-mutant astrocytoma patients. MGMT promoter methylation status was not prognostic for overall survival. CONCLUSIONS The CNS WHO grade is prognostic in patients with IDH-mutant astrocytoma. CDKN2A homozygous deletion and reduced LINE-1 methylation levels are linked to CNS WHO grade 4 and associate with shorter survival. These data serve to inform on clinical trial designs, e.g., using IDH inhibitors, in this patient population.
EPID-33. MORTALITY AND CAUSE OF DEATH RELATED TO CLINICAL AND GENETIC SEVERITY IN PATIENTS WITH NEUROFIBROMATOSIS TYPE 2 – SCHWANNOMATOSIS
Authors: Lisa Weigert, Anna Lawson McLean, Anna Freier, Said Farschtschi, Steffen Rosahl
Journal: Neuro-Oncology (2023)

Abstract OBJECTIVES This study aimed to investigate the circumstances of death in NF2 patients, focusing on clinical and genetic severity. METHODS Data from three major German NF2 centers were analyzed retrospectively. A total of 199 patients were included, with follow-up periods ranging from 6 months to 30 years. Disease severity was assessed using clinical and genetic classification scales with three grades each. At the time of data analysis, 36 patients had died in all three centers combined. RESULTS Of the 36 deceased patients, 47.2% had moderate clinical severity, 38.9% had severe disease, 13,9% were classified as grade 1. Genetic severity could be determined for 15 patients with 66.7% categorized as a moderate NF2 and 20.0% as genetically severe NF2. Only 13.3% had tissue mosaicism associated with a mild genetic severity. Patients with moderate clinical severity died at a mean age of 44.5 years (± 20.97), patients in grade 3 died at 46.89 years (± 11.71), and grade 1 patients died at 35.1 years (± 31.36) in this cohort. Patients with the highest genetic severity score died earlier (mean age = 35.5 years ± 2.29) than those with a moderate severity (51.3 years ± 21.65). The most common causes of death were malignant neoplasms, cerebral insults, and pneumonia, each accounting for three of the cases. Other causes of death included road traffic fatalities, septic shock, cerebral compression, and suicide, with 16.6% of cases involving attempted suicide. CONCLUSIONS The study emphasizes the need for a wider registry to assess prognosis, to stratify major risk factors causing mortality in NF2 and to verify correlations to clinical and genetic severity scales. Increased suicide and attempted suicide rates among NF2 patients highlight the importance of psychological counseling in patient management.
EXTH-24. FC-ENHANCED ANTI-CTLA-4 IMMUNE CHECKPOINT BLOCKADE AND ITS COMBINATION WITH ANTI-PD-1 WITH CONCOMITANT DOXORUBICIN AND ULTRASOUND-MEDIATED BBB OPENING: A NOVEL IMMUNOTHERAPY FOR GLIOBLASTOMA
Authors: Kwang-Soo Kim, Karl Habashy, Andrew Gould, Hinda Najem, Junfei Zhao, Christina Amidei, Ruth Saganty, Victor Arrieta, Crismita Dmello, Li Chen, Daniel Zhang, Brandyn Castro, Leah Billingham, Daniel Levey, Benjamin Morin, Miguel Muzzio, Michael Canney, Katy McCortney, Craig Horbinski, Peng Zhang, Jason Miska, Raul Rabadan, Amy Heimberger, Roger Stupp, Dhan Chand, Catalina Lee-Chang, Adam Sonabend
Journal: Neuro-Oncology (2023)

Abstract Despite the recent success of immune checkpoint blockade in various cancer types, glioblastoma (GBM) remains resistant to immunotherapy due to its immunosuppressive features and the poor penetration of systemic agents across the blood-brain barrier (BBB). Recent clinical trials demonstrated the unprecedented efficacy of Fc enhanced anti-CTLA-4, an anti-CTLA-4 antibody with enhanced affinity to Fcγ receptors (FcE-aCTLA-4), against immunologically inactive (‘cold’) tumors. This agent exhibits a high affinity for FcγRIIIA regardless of its polymorphic variants of FcgRIIIA that are known to influence the binding affinity and efficacy of conventional anti-CTLA-4 antibodies. We observed robust expression of FcγRIIIA in tumor-associated macrophages/myeloid cells (TAM) of human GBM, which was most pronounced in newly diagnosed GBM. FcE-aCTLA-4 demonstrated high-affinity binding to FcγRIV, the mouse ortholog of human FcγRIIIA, which was highly expressed on TAMs in mouse gliomas. We evaluated the efficacy of the murine homologous FcE-aCTLA-4 antibody as monotherapy and in combination with other treatments in several murine glioma models. FcE-aCTLA-4 selectively depleted CTLA-4 expressing intra-tumoral regulatory T cells (Tregs) via antibody-dependent phagocytosis by TAMs while spearing peripheral Tregs and other CD4+ T cell populations. In a cohort of 4 GBM patients, doxorubicin delivered with low-intensity pulsed ultrasound and microbubbles (LIPU/MB), a procedure that temporarily opens the BBB, upregulated FcγRIIIA expression on TAMs. Treatment of immunotherapy-resistant murine gliomas with a combination of FcE-aCTLA-4, anti-PD-1, and doxorubicin with concomitant LIPU/MB resulted in over 90% cure rates, which correlated with increased infiltration of activated CD8+ T cells in the brain, and complete rejection upon subsequent tumor rechallenge. Our findings indicate that FcE-aCTLA-4 exhibits a novel immunomodulatory function in GBM, and its therapeutic potential is significantly improved when combined with anti-PD-1, doxorubicin, and delivered by LIPU/MB. This therapy warrants further evaluation in clinical trials.
RBIO-02. NOVEL, QUIESCENT SUBPOPULATION EMERGES AFTER LOW-DOSE IRRADIATION OF GLIOMA STEM CELLS
Authors: Erika Lewis, Costanza Lo Cascio, James McNamara, Shwetal Mehta, Christopher Plaisier
Journal: Neuro-Oncology (2023)

Abstract Glioblastoma (GBM) tumors contain a subset of highly radiation resistant cells referred to as glioma stem cells (GSCs). We used single-cell RNA-seq (scRNA-seq) to characterize the transcriptional states that increase in size following GSC irradiation to further our understanding of the acute responses to radiotherapy. We treated two GBM patient-derived xenograft-derived GSC lines to low-dose irradiation (4 Gy). We then conducted scRNA-seq before irradiation and three days and one-week post-irradiation. As expected, the number of GSCs undergoing division through the cell cycle was drastically reduced relative to control conditions, and a subpopulation of GSCs with DNA damage response markers emerged after irradiation. Interestingly, we observed a novel, distinct subpopulation that was common between GSC lines, expanded after irradiation, and featured marker genes related to cell cycle arrest in response to external stressors. Gene regulatory network analysis identified transcription factors (TFs) likely to regulate these marker genes and potentially the dynamics of this subpopulation. The TFs were also related to cell cycle suppression and the overall expression state of these cells was similar to the quiescent Neural G0 state, indicating that our novel subpopulation may contain quiescent GSCs. In upcoming studies, we plan to perturb these TFs and marker genes to determine the importance of these genes in the GSC response to irradiation. Further exploration of this novel quiescent subpopulation may lead to new druggable targets that sensitize GBM tumors to radiotherapy.
CTNI-63. A PHASE IIA CLINICAL TRIAL FOR COMBINATION OF NAVIGATION-GUIDE FOCUSED ULTRASOUND AND BEVACIZUMAB FOR PATIENTS WITH RECURRENT GLIOBLASTOMA
Authors: Kuo-Chen Wei
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Bevacizumab (BEV), a vascular normalizing therapy that prolongs progression free survival (PFS) for patients with recurrent glioblastoma (rGBM). Focused ultrasound combines with microbubbles (MB-FUS), an emergent technology for targeted blood-brain barrier opening (BBBO), is under investigation for its combinatorial effect with current standard of care for GBM treatment. This study aims to evaluate the safety and efficacy of BEV + MB-FUS for treating patients with rGBM. METHODS This is a phase IIa, open-label, single-arm clinical trial (NCT04446416). Eligible patients received BEV (10 mg/kg), then MB-FUS with a MB dosage of 0.1 ml/kg and neuronavigation-guided FUS system (NaviFUS-001, NaviFUS, Taiwan). The MB-FUS is planned to be an add-on modality to the bi-weekly BEV therapy for up to 18 sessions (FUSBEV, 34 weeks). RESULTS Six patients underwent total 156 FUS-BEVs (26 times per patients). Three patients (50%) completed the trial protocol, 2 of another 3 patients had disease progression during the treatments, the remaining one patient was in stable disease. The mean progression free survival was 7.5 months. Among the 156 sessions of MB-FUS, there were 3 (1.9%) transient focal scalp pain related to heating. An evaluation of the MB-FUS penetrated regions revealed a significant normalization effect of T2 signal hyperintensity at beam-concentrated areas. CONCLUSIONS The PFS-6 was 67% in this study. RESULTS have demonstrated the safety, feasibility, and a potential to decrease edema by the mechanism of enhance bevacizumab delivery to the treated site. The preliminary results are encouraging. More data are needed to proof the efficacy of BEV-FUS on rGBM patients.
EXTH-18. DEVELOPMENT OF A TRANSGENIC MOUSE MODEL ENABLING COMPARATIVE ANALYSIS OF CHIMERIC ANTIGEN RECEPTOR (CAR)-EXPRESSING IMMUNE CELL POPULATIONS FOR CANCER IMMUNOTHERAPY
Authors: Ryusuke Hatae, Payal Watchmaker, Akane Yamamichi, Keith Kyewalabye, Kaori Okada, Su Phyu, Yitzhar Goretsky, Tiffany Chen, Pavlina Chuntova, Masaki Terabe, Hideho Okada
Journal: Neuro-Oncology (2023)

Abstract We reported the creation of C57BL/6J-background transgenic (Tg) mice carrying the anti-epidermal growth factor receptor (EGFR)vIII-CAR with CD3z-CD28-4-1BB downstream of a Lox-Stop-Lox cassette in the Rosa26 locus. Breeding these mice with CD4-Cre Tg allows rigorous and reproducible evaluation of CAR-T cell therapy in syngeneic models (Chuntova et al. Neuro-Onc 2022). As the extension of the approach, we crossed the EGFRvIII-CAR Tg mice with mice carrying Vav-Cre, which allowed the expression of anti-EGFRvIII CAR in all hematopoietic cells. In particular, we evaluated CAR-T, CAR-NKT, CAR-NK cells, and CAR-macrophages. CAR-NK cells displayed a robust antigen-specific cytolytic activity against EGFRvIII-expressing SB28 cells, comparable to CAR-T cells in vitro and mice bearing intracerebral EGFRvIII-expressing SB28 gliomas. Remarkably, CAR-NKT cells produced higher levels of inflammatory cytokines when co-cultured with EGFRvIII-expressing SB28 cells, such as IFN-g, Perforin, IL4, and IL17. On the other hand, despite their in vitro cytotoxic effects against SB28 cells, CAR-NK cells failed to mediate a therapeutic response in mice bearing intracerebral glioma. Future studies will be directed at improving the in vivo persistence of CAR-NK cells using engineered cytokines, such as IL-2 superkine. In addition, we extensively investigated CAR-macrophages in vitro and in vivo. Unfortunately, we did not observe significant CAR-specific anti-tumor effects. Consequently, we modified the intracellular domain of CAR from CD3z-CD28-4-1BB to CD3z alone. This alteration led to increased TNF-α production through CAR signaling. This transgenic mouse model offers rigorous and reproducible evaluations of CAR-expressing hematopoietic cells. Furthermore, the model provides a platform for developing combination therapies, such as CAR-T plus CAR-NKT or CAR-T plus CAR-NK cells, with potential implications for enhanced cancer treatment strategies.
MODL-12. REGULATION OF OLIGODENDROGLIAL PROGENITOR CELL (OPC) CELL FATE IN DIFFUSE MIDLINE GLIOMA (DMG) BY THE HOMEOBOX TRANSCRIPTION FACTOR DLX2
Authors: Liam Furst, Enola Roussel, Ryan Leung, Ankita George, Ron Firestein, Maree Faux, David Eisenstat
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline glioma, K27-altered (DMG) is a treatment resistant, uniformly fatal cancer that arises predominantly in children. 80% of patients with DMG harbor K27M mutations in canonical histone variants H3.3 and H3.1, leading to global epigenetic dysregulation and an oligodendroglial progenitor cell (OPC) transcriptional profile. DLX2 is a homeobox transcription factor that directly represses OPC cell fate and promotes a GABAergic interneuron cell fate during neurogenesis. Our lab has previously identified DLX2 transcription factor occupancy of genes required for OPC differentiation in vivo (Olig2, Nkx2.2, Myt1, Plp1), and shown that co-expression of DLX2 to target sequences reduced reporter gene expression in vitro. Likewise, increased expression of Olig2, Nkx2.2, and Plp-1 are observed in a Dlx1/Dlx2 double knockout (DKO) mouse model. Transient overexpression of a Dlx2-GFP construct into cells of a genetically engineered mouse model (GEMM) of DMG resulted in increased expression of Gad1/2 isoforms and decreased Olig2 and Nkx2.2, global restoration of H3K27me3, and a reduction in migration, invasion, and colony formation in vitro. Inverse expression of DLX2 and OLIG1/2 was observed in a bulk RNAseq database of 45 human DMG cell lines. We have established a pipeline to evaluate cell fate changes following changes in DLX2 expression levels. OLIG1/2high/DLX2low DMG expressing cell lines underwent stable transfection of a DLX2-mCherry overexpression construct. Successful alteration of DLX2 expression was confirmed by qPCR and immunoblot in knockout and overexpressing human DMG cell lines. Analysis of histone marks (H3K27me3, H3K27ac), K27M, and OPC signature genes will be presented with comparison of altered OPC genes from the DKO mouse as determined by RNA-seq. The manipulation of DLX2 expression in human DMG cells in vitro and in vivo provides a model system for assessing the contribution of a homeobox transcription factor required for neurogenesis to cell fate regulation and effects on tumorigenicity in DMG.